This repository contains a docker configuration setup to build the full CRN stack. This includes:
You must configure the system by copying config.env.example to config.env and .env to .env.example and filling in any empty values. Other values may be modified, but changes to the defaults could cause issues. Below is a list of descriptions of each variable.
| variable | description |
|---|---|
| SCITRAN_URL | The url where SciTran is listening |
| SCITRAN_RUNTIME_PORT | The Port SciTran will listen on |
| SCITRAN_CORE_DRONE_SECRET | A secret string shared between this service and SciTran |
| SCITRAN_PERSISTENT_DATA_PATH | The file system location of SciTran's data store |
| SCITRAN_PERSISTENT_DB_URI | The URI to the mongo database SciTran will use |
| SCITRAN_AUTH_CLIENT_ID | The OAuth client ID used to authenticate w/ SciTran |
| SCITRAN_AUTH_ID_ENDPOINT | The OAuth ID endpoint of the auth provider |
| SCITRAN_AUTH_VERIFY_ENDPOINT | The OAuth verify endpoint of the auth provider |
| CRN_SERVER_URL | The url where this service is listening |
| CRN_SERVER_AGAVE_URL | The root url to the AGAVE API |
| CRN_SERVER_AGAVE_USERNAME | An AGAVE API username |
| CRN_SERVER_AGAVE_PASSWORD | The corresponding AGAVE API password |
| CRN_SERVER_AGAVE_CLIENT_NAME | The name of a registered AGAVE client |
| CRN_SERVER_AGAVE_CLIENT_DESCRIPTION | The description of the AGAVE client |
| CRN_SERVER_AGAVE_CONSUMER_KEY | The AGAVE client API key |
| CRN_SERVER_AGAVE_CONSUMER_SECRET | The AGAVE client API secret |
| CRN_SERVER_AGAVE_STORAGE | The root path of the associated AGAVE storage system |
| CRN_SERVER_MAIL_SERVICE | The name of the mail service for email notifications |
| CRN_SERVER_MAIL_USER | The username for the mail service |
| CRN_SERVER_MAIL_PASS | The password for the mail service |
| AWS_ACCESS_KEY_ID | Access key id for AWS account |
| AWS_SECRET_ACCESS_KEY | Secret Access Key for AWS account |
| AWS_REGION | AWS region |
| AWS_S3_DATASET_BUCKET | S3 bucket name where datasets are stored |
| AWS_S3_ANALYSIS_BUCKET | S3 bucket name where job output is stored |
| AWS_BATCH_QUEUE | Job Queue name on AWS batch |
| GOOGLE_TRACKING_ID | Google Analytics tracking ID |
| variable | description |
|---|---|
| CRN_BRANCH | The branch to build the CRN server and app from |
| PERSISTENT_DIR | The local directory to mount persistent data to |
| SFTP_USER | The local user used for SFTP authentication |
If you would like to be able to expose datasets over SFTP to AGAVE you must ensure your BIDS_CORE_PERSISTENT_DIR and CRN_SERVER_PERSISTENT_DIR are accessible as AGAVE storage systems.
/srv/bids-core/persistent/data/srv/crn-server/persistent
To build the CRN stack you must first install docker. Once you've updated the configuration, from the root of this project you can run docker-compose build to build all of the containers. This may take a while. Once your containers are built you can run docker-compose up and the application will be available at the localhost's port 80.